RetrogeneDB ID: retro_ecab_470

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 19:14204673..14205023(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: ANAPC15
• Ensembl ID: ENSECAG00000021041
• Aliases: None
• Description: anaphase promoting complex subunit 15 [Source:HGNC Symbol;Acc:24531]

Sequence

>retro_ecab_470
ATGTCCACCTTATTGCCCTCACTCTTGCCCCATGTGACTGAGATACTGTGGTTTAATCTGGATTGGCCCTGTGTGGAGGA
GAGAGCTGCAGCAGCAGGAACAACAGCAAGCCTGACTCTAGAGCACCATAGAGAAAAACAACAACTTGGTATCTATTGAC
AAGCCCGTGTCAGAGCACTATGATGACAAGAAAGGGGAGGAGGATGAAGGTGAAGGGATAGCGAAGACTCAGAGGATGAT
GAGGACATCAGGATATGGATGAGATAAGTGATTACAGTGAGTAGCCTGATGATGGAGAGGTCATTGAGGTGGACATGGAA
GGCAACAAACAGGATCAGGACCAGTGGATA

Alignment

ORF - retro_ecab_470 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 99.17 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSTLFPSLFPRVTETLWFNLDRPCVEETEL-QQQEQQHQAWLQSIAEKDNNLVPIGKPASEHYDDEEEED
          MSTL.PSL.P.VTE.LWFNLD.PCVEE....QQ..Q..QA.L.S..EK.NNLV.I.KP.SEHYDD...E.
Retrocopy MSTLLPSLLPHVTEILWFNLDWPCVEERAA>QQEQQ--QA*L*STIEKNNNLVSIDKPVSEHYDDKKGEE

Parental  EDDD-EDSEEDSEDDEDM-QDMDEMNDYNESPDDGEVNEVDMEGNEQDQDQWM
          ......DS.EDSEDDED..QDMDE..DY.E.PDDGEV.EVDMEGN.QDQDQW.
Retrocopy DEGE<RDS-EDSEDDEDI<QDMDEISDYSE*PDDGEVIEVDMEGNKQDQDQWI

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP021940_articular_cartilage	0.00 RPM	10.21 RPM
SRP021940_cerebellum	0.00 RPM	12.57 RPM
SRP021940_embryo	0.00 RPM	22.22 RPM
SRP021940_placental_villous	0.00 RPM	9.29 RPM
SRP021940_synovial_membrane	0.00 RPM	9.72 RPM
SRP021940_testis	0.00 RPM	69.51 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_470 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_470 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_470 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1999
Pongo abelii	retro_pabe_2388
Bos taurus	retro_btau_269

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010843	1 retrocopy	retro_amel_298,
Bos taurus	ENSBTAG00000002999	2 retrocopies	retro_btau_252, retro_btau_269,
Canis familiaris	ENSCAFG00000005781	1 retrocopy	retro_cfam_1752,
Equus caballus	ENSECAG00000021041	1 retrocopy	retro_ecab_470 ,
Felis catus	ENSFCAG00000005321	1 retrocopy	retro_fcat_1350,
Homo sapiens	ENSG00000110200	1 retrocopy	retro_hsap_4780,
Gorilla gorilla	ENSGGOG00000012501	2 retrocopies	retro_ggor_1999, retro_ggor_2977,
Myotis lucifugus	ENSMLUG00000014120	1 retrocopy	retro_mluc_238,
Macaca mulatta	ENSMMUG00000016270	1 retrocopy	retro_mmul_2551,
Mustela putorius furo	ENSMPUG00000010260	1 retrocopy	retro_mputfur_596,
Nomascus leucogenys	ENSNLEG00000017234	1 retrocopy	retro_nleu_1100,
Pongo abelii	ENSPPYG00000003646	2 retrocopies	retro_pabe_2388, retro_pabe_3720,
Pteropus vampyrus	ENSPVAG00000015797	1 retrocopy	retro_pvam_404,
Sorex araneus	ENSSARG00000004171	2 retrocopies	retro_sara_444, retro_sara_686,
Tarsius syrichta	ENSTSYG00000014179	1 retrocopy	retro_tsyr_35,
Tursiops truncatus	ENSTTRG00000010773	1 retrocopy	retro_ttru_277,